Blages

Friday, August 31, 2012

So, here are two videos that are making the rounds on the internet today. Although at first glance, they may be hard to distinguish, if you look closely, you will find that one is actually a video of two hamsters spinning insanely around an exercise wheel, while the other is Clint Eastwood speaking at the Republican National Convention.

I won't spoil the game by telling you in advance which is which. See if you can spot the difference yourself!

Wednesday, August 29, 2012

So, you know how Reddit does this question and answer thing, where famous and/or knowledgable people log on and take questions from the Reddit community? Well, much to the delight of the internet, today at 4:30 Eastern, President Obama held one of these.

In case you missed it, here are a few of the highlights from the ensuing conversation.

I'm surprised the username PresidentObama was even available. Or is the man powerful enough to just take it over anyway? I'd hate to see the leader of the free world reduced to taking a username like TheRealPresidentObama or POTUS69 or xx_BarackObama_xx or something.

Internet freedom is something I know you all care passionately about; I do too. We will fight hard to make sure that the internet remains the open forum for everybody - from those who are expressing an idea to those to want to start a business. And although there will be occasional disagreements on the details of various legislative proposals, I won't stray from that principle - and it will be reflected in the platform.

Making sure we stay at the forefront of space exploration is a big priority for my administration. The passing of Neil Armstrong this week is a reminder of the inspiration and wonder that our space program has provided in the past; the curiosity probe on mars is a reminder of what remains to be discovered. The key is to make sure that we invest in cutting edge research that can take us to the next level - so even as we continue work with the international space station, we are focused on a potential mission to a asteroid as a prelude to a manned Mars flight.

So, Sam Arbesman has a post up at Wired where he discusses a recent study on the work habits of scientists in around the world. As a proxy for "working," the authors look at the pattern of downloads of papers or book chapters from Springer. The work makes use of a cool real-time mapping of IP addresses accessing those papers. If you want to see what it looks like, check it out here: http://realtime.springer.com/map.

They do a more detailed analysis of the top three countries (in terms of total number of downloads in about a week's worth of data), the US, Germany, and China. Correcting for time zone differences, they find these patterns:

On the left side, each line corresponds to a different day, with the more solid lines being weekends, and the thinner ones being weekdays. On the right, the weekends and weekdays are averaged.

A couple of things that will probably come as no surprise to most of the academics out there.

(1) the daily hump starts picking up around 9 or 10 in the morning, and carries on until nine or ten at night.

(2) the weekday hump is bigger during traditional "working hours", but evening work hours are pretty consistent throughout the week.

Interesting cultural differences pop out that might not be as predictable. It looks like China has longer and/or more simultaneous breaks for lunch and dinner. (Although, given the common practice, at least in the US, of eating lunch at your computer, maybe the lack of those dips in the top panel are somewhat predictable.) Americans seem to be working a lot more in the middle of the night compared with their German and Chinese counterparts, while the Chinese seem to show less of a difference between weekday and weekend work habits.

The authors' conclusion, and one that is echoed in Sam Arbesman's commentary, is that this work pattern is consistent with what most academic scientists would probably tell you. Academia is a full-time job. And not a full-time job in the sense of a forty-hour work week, but a full time job as in, you sleep, eat, and work.

So is that a good thing or a bad thing? Well, on the one hand, you've got all of these highly trained, highly educated people working really hard and getting paid not a whole awful lot on a per-hour basis. Good deal, right?

On the other hand, it leads to a really crappy lifestyle, where the long hours come at the expense of time spent with family, hobbies, or even taking an interest in subjects outside of the very narrow range defined by your research. If you care about a broader definition of human happiness, one that treats people as an end rather than a means, this is not a great way to structure your industry.

Beyond that, it is important to remember that science, like all academic fields, is a fundamentally creative enterprise, and working longer hours does not necessarily translate into better results. Creativity has to be fueled by experience, and a broader range of experience can lead to asking more interesting questions and coming up with more original answers to those questions. The pressures that lead people to download papers from Springer from morning till night don't necessarily lead to the best science.

I should note that Sam's coverage also includes a plug for the Ronin Institute, because Sam is a freakin' rock star!

Friday, August 24, 2012

So, this morning, Mitt Romney came up with an interesting new strategy designed to divert attention from his quite possibly illegaltax history, his party's extremist abortion position, and general unlikability: he launched a stand up comedy routine. Speaking in Michigan, he cracked this gem straight out of the Birther Bathroom Jokebook:

No one's ever asked to see my birth certificate.

See, it's hilarious because he's white! And Obama is black!

So, what other bon mots can we expect from Romney as he takes his routine to Tampa? Here at Lost in Transcription, we've received this advance list of jokes, which were allegedly written by Dane Cook's racist brother, and will be dropped at the Republican National Convention next week to much hooting and cheering from the hungover and overstimulated delegates. Here are a few of the most hilarious:

No one ever arrested me in Arizona!

No one ever stopped and frisked me in New York!

No one ever renditioned me to Guantanamo!

No one ever questioned my right to stand my ground!

No one ever paid me 77 cents on the dollar to do the same job!

No one ever assumed I was the gardener!

No one ever put my grandparents in an oven!

No one ever questioned my right to get married!

No one ever put my family on a reservation!

No one ever held me down and cut my hair!

No one ever denied me health insurance!

See, they're all so funny, because Mitt has lived a life of incredible privilege!

How about you, readers? Have your inside sources uncovered any material? If so, please share it in the comments.

Wednesday, August 22, 2012

So, as you are well aware, a couple of days ago, human-shaped pile of garbage Todd Akin articulated his belief that "legitimate rape" rarely leads to pregnancy, due to the magical uterine "shutting that whole thing down" properties of the uterus. Here at Lost in Transcription, we discussed the fact that there are some species that do, in fact, exhibit the capacity for "post-copulatory female choice." However, humans are not one of these species, unless you count the set of medical interventions that Akin is trying to outlaw (along with Romney, Ryan, and the official Republican party platform).

If you're interested, Kate Clancy wrote up an excellent summary of the actual science on the topic of pregnancy and rape.

Jesse Bering (an evolutionary psychologist who has been featured on this blog previously) also weighed in on the science, using twitter to point to an article that had recently written on "Darwin's Morning After Pill." In the article, Bering outlines an argument for the adaptive value of preeclampsia. The argument features "seminal priming theory," which Bering calls "criminally unread," and which has been promoted by Gordon Gallup (who, like a certain goat I know, has an adaptationist story for just about everything).

Roughly, the argument is this. Women don't want to let a man get them pregnant unless they are certain that the man is going to stick around for the long haul. So, you want to have a biological mechanism that prevents pregnancy from one-night stands, but encourages pregnancy when you are in a committed relationship. Preeclampsia is a convenient (if life threatening) way for mother nature to terminate your pregnancy when it would be better not to have a baby. Therefore, preeclampsia should be more common for pregnancies resulting from sex with an unfamiliar male. Preeclampsia should be less common when it is the product of a long-term sexual relationship.

The proposed mechanism is that exposure to a male's semen sort of habituates the female to the biochemistry of that particular male. Preeclampsia is associated with certain inflammatory features that share some similarities with an immune response. In that sense, preeclampsia is sometimes thought of as the mother rejecting the foreign body of the fetus, sort of like how one might reject a transplanted organ. The idea, then, is that through exposure to the male's semen, the female ratchets down this response, thereby allowing the pregnancy to move forward.

One way of thinking about preeclampsia is as the rejection of an alien body by the mother

Jeremy Yoder has written a nice piece detailing how, even if we accept all of this, it is ridiculous to think of this mechanism as an adaptation. In particular, even under the most generous set of assumptions, natural selection acting on such a mechanism would be vanishingly small. And, of course, even to get there, you have to buy the typical evolutionary psychology assumption of an "environment of evolutionary adaptation" that looks an awful lot like the normative middle-class, suburban values of 1950s television America.

There are a few lines of evidence that are cited (by Bering, and in general) in support of the idea. The bulk of the evidence hinges on the observation that changing partners increases a woman's probability of preeclampsia. For example, if your second pregnancy has the same father as your first pregnancy, you are less likely to develop preeclampsia than if the two pregnancies have different fathers. This is a finding that has been replicated a number of times, and with very large samples, so that's pretty solid, right?

Actually, no. While the association between paternity switch and preeclampsia is true, it probably doesn't mean what Bering and Gallup think it means, and the relevant data doesn't actually support the seminal priming theory.

The problem is that a change in paternity correlates with time between pregnancies. So, if your two kids have different fathers, it is more likely that the two pregnancies were spaced farther apart. My reading of the literature is this: in every case where there is an association between paternity switching and preeclampsia, the study has not separately controlled for time between pregnancies. In each study where time between pregnancy is explicitly controlled for, the association with paternity switching vanishes. (See, e.g., this or this.)

In fact, controlling for time between pregnancies, if you have preeclampsia in your first pregnancy, switching partners actually makes you less likely to have preeclampsia in your second one. Don't get too excited though. The converse is also true. If you don't get preeclampsia in one pregnancy, switching partners makes you more likely to get it in the next one.

What that suggests (to me, anyway), is that some fathers are more likely to produce preeclampsia than others (or, alternatively, that the probability of preeclampsia depends on some interaction between the maternal and paternal genotypes). According to this explanation, if you don't get preeclampsia, it means that you and your partner are at low risk. If you switch partners, though, you go back into the standard risk pool. (This interpretation is also consistent with this study, which followed fathers.)

There are a few other lines of evidence, which are cleaner in their implications. One study on artificial insemination finds preeclampsia more often in cases where the woman was inseminated with a stranger's sperm than in cases where she was inseminated with her partner's. There is also a study that finds that frequent oral sex correlates with a reduced risk of preeclampsia. (That's her performing oral sex on him, not the other way round.) Does the frequency of oral sex correlate with the spacing between kids? I don't know. I'm hoping that some of you will weigh in on that in the comments.

Males ingesting female gametes also has well documented health benefits.

The problem with these studies is that, unlike the partner-switching studies, we're looking at small numbers. Whether or not they will hold up under more extensive analysis it not yet clear.

My read on the whole thing? At the moment, the data just isn't there. All that exists in support of the seminal priming theory is an adaptationist fairy tale and a couple of small studies that have yet to be reproduced.

Oh, and also a whole bunch of studies that, if you cherry pick from among them, and ignore all of the studies that contradict them, support the theory. Of course, that's pretty much true of any theory, which is exactly why evolutionary psychology continues to be such a booming field.

Tuesday, August 21, 2012

So, welcome back to installation #2 in The case for independent scholarship, the new series where I explain why you should quit assuming that scholarly research needs to be limited to the university system. In fact, independent scholarship provides a number of advantages over the standard model.

Today, we're going to focus on the administrative bloat that has overcome the university system. Specifically, I want to draw your attention to statistics on the California State University system. These data have been collected and written about by Ralph Westphal, a Professor in the Computer Information Systems Department at California Polytechnic University, Pomona.

Before I show you the statistics, though, I want you to ask yourself, how many administrators and other, non-academic professionals does a university need for each faculty member? What would be a reasonable ratio of academic to non-academic employees?

Clearly, there is a certain amount of support required to maintain facilities, to manage offices and accounts, and so on. But how many, would you say? Here are the numbers (from this document) for the entire California State University system for the 1975-76 academic year:

Faculty (all ranks): 18,406

Service and maintenance: 3,260

Skilled crafts: 883

Technical and paraprofessional: 3,246

Clerical and secretarial: 6,920

Managerial and professional: 3,800

So, what do you think? Does this seem reasonable? Roughly speaking, for every four faculty members, there are three non-faculty employees doing all of the jobs that keep the university running smoothly, and therefore allowing the faculty to pursue the fundamental goals of the university: teaching and research.

What about now? Well, if we fast forward thirty-some years to the most recent data provided in the same document, we find that, in the faculty increased to 23,581. That's a 28% increase in the size of the faculty. This goes along with a 54% increase in the number of full-time student equivalents (as per Westphal). Clearly, that means there are fewer teachers per student, but, you know, times are tough, budgets are crunched, and so on.

Faculty (all ranks): 23,581

Service and maintenance: 2,170

Skilled crafts: 1,045

Technical and paraprofessional: 3,105

Clerical and secretarial: 4,145

Managerial and professional: 12,183

Note:

The "skilled crafts" category has grown roughly in proportion to the number of faculty.

The "service and maintenance," "technical and paraprofessional," and "clerical and secretarial" categories have all actually shrunk in absolute numbers.

The big winner, of course, is "managerial and professional," which increased to 3.2 times its 1975-76 size.

So, what we see is a faculty that has failed to keep pace with the growth in the student population. We see support staff that not only has failed to keep up with the growth in faculty and students, but has actually been slashed. In contrast, the administrative ranks have become bloated beyond belief, to the point where there is nearly one "managerial" or "professional" employee for every two faculty members.

Westphal also points out that while the administration is willing to cut academic programs, there is little hope of reversing the administrative bloat. This is from the LA Times, quoting Cal Poly Pomona's Provost, Marten L. denBoer:

He said administrative functions will be reviewed and probably pared, but he rejects the argument that significant cuts can be made in that area. "The lights have to stay on, and someone has to maintain the computer system," he said. "These are people who work very hard and have to be properly compensated."

Note that the people who, say, keep the lights on, are not the problem.

Fundamentally, the problem is that people in administration see a valuable role for administrators, and devalue everything done by everyone else. So, when cuts have to be made, and you leave those cuts up to administrators, it is no surprise that administration is the last thing on the chopping block.

So, here's a question for you. If you are a donor, or a taxpayer, or a funding agency, why would you allow your resources to get eaten up by institutions that devote less and less of their effort to the research and teaching that you want to support?

Monday, August 20, 2012

So, you're doubtless already well versed in the intellectual train wreck that is Todd Akin, the Missouri Republican who thinks that "legitimate rape" can not lead to pregnancy. More specifically, here's the money quote via TPM:

“First of all, from what I understand from doctors [pregnancy from rape] is really rare,” Akin told KTVI-TV in an interview posted Sunday. “If it’s a legitimate rape, the female body has ways to try to shut that whole thing down.”

Well, good news, internet! Akin now has his own Tumblr (fromtalkingtodoctors.tumblr.com), filled with all the other things he's learned from talking to doctors. Here are a few samples for you.

So, as regular readers already know, I have recently founded a nonprofit institute that is dedicated to supporting and promoting independent scholarship -- that is, scholarly research outside of the standard system of research universities and government laboratories.

(Sounds cool, right? Want to know more? Drop by the webpage of the Ronin Institute.)

Why do we need to promote independent scholarship? Well, there are a lot of great reasons, and they're the topic of my new series: The case for independent scholarship, where I'm going to break those reasons down for you. But, for those of you who can't wait to read about all of those compelling reasons in detail, here's a précis of the coming argument. Whether you are a scholar yourself, a financial supporter of scholarship, or just someone who believes that things should be done better in the future than in the past, here is why you should be looking beyond the standard academic model.

Independent scholarship is cheaper and more efficient. Research universities and government laboratories support huge, bureaucratic infrastructures that must be fed by siphoning funding away from research.

Independent scholarship is more democratic. Along with the bureaucracy of large research institutions comes hierarchical structures that can limit academic freedom.

Independent scholarship is more humane. The independent-scholarship model avoids many of the problems of the traditional academic lifestyle, which is often at odds with other goals, such as being an involved parent. Independent scholars can set their own hours to accommodate other priorities, and are not as geographically restricted as traditional academics -- thus avoiding the academic "two-body problem."

Independent scholarship is more transdisciplinary. The departmental structure in universities -- or whatever bureaucratic structure exists in a particular institution -- tends to create artificial barriers to exploration and collaboration. Some institutions have taken steps to encourage interdisciplinary research, but the independent scholar is naturally situated to pursue the most interesting questions without any artificial constraints.

Independent scholarship can exploit untapped intellectual resources. In the United States alone, there are tens of thousands of people with PhDs who are not making use of their PhD training. The independent-scholarship model allows people with training in and passion for a subject to contribute to their field, even if only in a part-time capacity.

Independent scholarship does not need to be profit driven. Increasingly, hiring and tenure decisions at universities are driven by funding considerations. Independent scholarship can be driven by important questions, rather than by the need to develop and justify large research budgets.

Independent scholarship honors donor intent. For philanthropists who support research, donations to universities are always problematic, since the fungibility of funds means that donations rarely go 100% to support the program(s) that the donor cares about. Independent scholarship can be structure in a scalable way, so that donations translate directly to increased support for those research projects that are most important to the donor.

Independent scholarship is more open. The independent-scholarship model aims to break down the distinctions between the ivory tower of academia and the broader population of intelligent, educated individuals who are eager and able to contribute to scholarly discourse.

In upcoming installations of this series, I will devote one or more posts to each of these bullet points and more, bringing in some detail and statistics to illustrate each.

So, maybe you've seen the news today about Representative Todd Akin. He's the republican nominee for Senate in Missouri, running this year against Claire McCaskill. In an interview he said that he opposed abortion in all circumstances, with no exception for rape, because rape does not lead to pregnancy, see, because, "If it's a legitimate rape, the female body has ways to try to shut that whole thing down." (Quotes on Jezebel, video here.)

After realizing that he sounded like a complete shithead, even for a contemporary Republican (and probably after receiving a scolding from national Republicans), he issued a statement in which he claims that he "misspoke," which is politician speak for, "I accidentally said what I actually thought, and then discovered that it will negatively impact my election chances, so I'm going to lie now. No backsies!"

Although, to be fair to Akin, nowhere in his statement did he back down from the position that abortion should be outlawed without exception, merely that he would advocate for "justice." Also, jobs!

Setting aside for the moment the woeful state of politics, is it true, or even possible, that the female body could have "ways to try to shut that whole thing down"?

Actually, in a lot of non-human animals, something sort of like that does exist.

In species where polyandry (where females mate with multiple males) is common, there is often competition for reproductive access both before and after copulation, where one male may participate in a larger share of a female's reproduction. In many cases, this is going to be something like sperm competition, where differential reproductive success depends on traits associated with the sperm, and by extension, with the competing males. This is not really what we're talking about, though.

In a few cases, you can actually get "post-copulatory female choice," where it is clearly the female deciding whether or not to allow fertilization. One such set of cases occurs in some spiders and crickets, where the male transfers a spermatophore to the female. This is basically a bag full of sperm that is attached to the female during copulation. She may then modulate the success of the sperm through the amount of time she permits it to remain attached to her.

For example, here's a paper on field crickets that shows not only that females modulate spermatophore retention time in response to male song quality, but that this modulation is contingent on the female's prior experience. This is important because it emphasizes the aspect of female choice.

But what about humans? Well, actually, yes. Human females have the capacity to engage in post-copulatory female choice, such that they do not necessarily have to give birth to their rapist's child. It's called safe, legal abortion. It still exists in this country, but if too many more Todd Akins get elected, the American female body will no longer have "ways to try to shut that whole thing down."

Thursday, August 2, 2012

So, one of the most interesting questions in evolutionary biology is the origin of collective behaviors. This can be the complex division of labor that we see in social insects and human societies, flocking behavior in migratory birds, or microbial formation of biofilms. It can be predators engaging in collective hunting, or prey engaging in collective being hunted. It's this last one that we're going to be talking about today.

As with many questions in evolutionary biology, there are a couple of dimensions that people are interested in untangling: proximal and ultimate causation. Proximal explanations focus on the "how" part of the solution, as in, "what are the molecular, genetic, etc. mechanisms and environmental cues that result in this behavior?" Ultimate explanations focus on "why," in the evolutionary sense of "what were the selective pressures that led to the evolution of this behavior?"

Herding or flocking behavior is a classic case. For example, why do sheep hang out in a big group, in contrast to say, leopards, which tend to be pretty solitary? There are a number of possible (and not mutually exclusive) ultimate explanations, but the most talked about one is probably defense against predators.

Back in the mid-twentieth century, it was common for biologists to talk in fairly loose terms about collective behaviors having evolved as a result of their benefits to the group. Then, in 1966, G. C. Williams published Adaptation and Natural Selection, which dropped a lot of truth into the community. In particular, it emphasized the gene-centered view of natural selection that hit the public consciousness with Richard Dawkins's 1976 book, The Selfish Gene, and which has remained the dominant paradigm in evolutionary biology ever since.

Williams demonstrated that group selection, while possible, will generally be a much weaker force than selection acting on the individual. Therefore, it is good practice to look for evolutionary explanations at this lower level. Given plausible adaptive stories at the individual and group levels, one should favor the individual-level story. While the two stories might not be mutually exclusive, individual-level selective pressures are more likely to have played an important role in the evolution of any particular trait than group-level selective pressures (all else being equal, of course).

In 1971, W. D. Hamilton published a theoretical analysis that brought this individual-level perspective to herding behavior. Hamilton argued that all you need is for animals to be trying to evade predators as individuals. If there are other individuals of their type around, they just need to try to position themselves between other individuals. Here's how Hamilton draws it:

This frog wants to position itself between the two frogs on the right. That way, when the sea snake comes up, it will eat one of the frogs at the edge, and the one in the middle will be safe.

All you need is for everyone to follow one simple rule: when a predator comes, position yourself between two other individuals. What you get then is a tight cluster of individuals.

You can actually try this at home. You probably need about eight or ten people. So, most of you might not be able to try this at home, but you could maybe try it at school or work. Have each person pick two other people in the group (but don't tell who your picks are). Then, everyone tries to get between the two people they picked. What you'll get is something a lot like a cluster of frogs climbing all over each other to get away from a sea snake.

Frogs maneuvering to get between other frogs results in the formation of a clusterf**k of frogs. I know, right? I was surprised, too, but my herpetologist friends assure me that "clusterf**k" is the official collective noun for a group of frogs. Don't even ask about sea snakes. You don't want to know.

Bonus activity: after you've disentangled yourselves from the frogpile, try this one. Each person picks two people again, labeling them "A" and "B" (in your head). Again, no one needs to say whom they picked. Now, each person should position themselves so that their "A" person is between them and their "B" person. If it helps, imagine that "A" is Mitt Romney, that "B" is the American People, and you are Mitt's tax returns. Your job is to position yourself so that Mitt keeps the American People from seeing you. I won't spoil how it comes out.

So, Hamilton's model provides a nice, simple model that can produce the observed behavior. The model is attractive because (1) it requires selection only at the level of the individual, and (2) it requires each individual only to follow a very simple behavioral rule. The collective behavior is an emergent property requiring no coordination at the group level.

Now, there's a new paper out that is attempting to look at this empirically, in sheep. The study involves strapping adorable GPS backpacks on a bunch of sheep (Figure 1c, below) and then letting a sheepdog chase them around.

You can look at the movies here. It's only a brief communication, and does not really nail anything down, but the authors interpret their results as broadly consistent with the selfish herd model. In particular, they are able to see that individual sheep seem to be trying to get to the center of the flock.

The cool thing is more the potential for this type of experiment. Yes, Hamilton's model is attractive and parsimonious, but if we want to understand the rules that actually govern the behavior of sheep when they are faced with a predator (or, in this case, an annoyator), we will need to get good quantitative data on individual behaviors in a variety of contexts.

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